Golang linear.NewSeq函数代码示例

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本文整理汇总了Golang中github.com/biogo/biogo/seq/linear.NewSeq函数的典型用法代码示例。如果您正苦于以下问题：Golang NewSeq函数的具体用法？Golang NewSeq怎么用？Golang NewSeq使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。

在下文中一共展示了NewSeq函数的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Golang代码示例。

示例1: init

func init() {
	var err error
	m, err = NewMulti("example multi",
		[]seq.Sequence{
			linear.NewSeq("example DNA 1", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.DNA),
			linear.NewSeq("example DNA 2", []alphabet.Letter("ACGGTGACCTGGCGCGCAT"), alphabet.DNA),
			linear.NewSeq("example DNA 3", []alphabet.Letter("ACGATGACGTGGCGCTCAT"), alphabet.DNA),
		},
		seq.DefaultConsensus)

	if err != nil {
		panic(err)
	}
}

开发者ID:gordon，项目名称:biogo，代码行数:14，代码来源:multi_example_test.go

示例2: TestReadFasta

func (s *S) TestReadFasta(c *check.C) {
	var (
		obtainN []string
		obtainS [][]alphabet.Letter
	)

	for _, fa := range fas {
		r := NewReader(bytes.NewBufferString(fa), linear.NewSeq("", nil, alphabet.Protein))
		for {
			if s, err := r.Read(); err != nil {
				if err == io.EOF {
					break
				} else {
					c.Fatalf("Failed to read %q: %s", fa, err)
				}
			} else {
				t := s.(*linear.Seq)
				header := t.Name()
				if desc := t.Description(); len(desc) > 0 {
					header += " " + desc
				}
				obtainN = append(obtainN, header)
				obtainS = append(obtainS, t.Slice().(alphabet.Letters))
			}
		}
		c.Check(obtainN, check.DeepEquals, expectN)
		obtainN = nil
		for i := range obtainS {
			c.Check(len(obtainS[i]), check.Equals, len(expectS[i]))
			c.Check(obtainS[i], check.DeepEquals, expectS[i])
		}
		obtainS = nil
	}
}

开发者ID:gordon，项目名称:biogo，代码行数:34，代码来源:fasta_test.go

示例3: TestReadFromFunc

func (s *S) TestReadFromFunc(c *check.C) {
	var (
		obtainNfa []string
		obtainSfa [][]alphabet.Letter
	)

	sc := seqio.NewScannerFromFunc(
		fasta.NewReader(
			bytes.NewBufferString(testaln0),
			linear.NewSeq("", nil, alphabet.Protein),
		).Read,
	)
	for sc.Next() {
		t := sc.Seq().(*linear.Seq)
		header := t.Name()
		if desc := t.Description(); len(desc) > 0 {
			header += " " + desc
		}
		obtainNfa = append(obtainNfa, header)
		obtainSfa = append(obtainSfa, t.Slice().(alphabet.Letters))
	}
	c.Check(sc.Error(), check.Equals, nil)
	c.Check(obtainNfa, check.DeepEquals, expectNfa)
	for i := range obtainSfa {
		c.Check(len(obtainSfa[i]), check.Equals, len(expectSfa[i]))
		c.Check(obtainSfa[i], check.DeepEquals, expectSfa[i])
	}
}

开发者ID:gordon，项目名称:biogo，代码行数:28，代码来源:seqio_test.go

示例4: TestReadFasta

func (s *S) TestReadFasta(c *check.C) {
	r := fasta.NewReader(strings.NewReader(fa), linear.NewSeq("", nil, alphabet.Protein))
	m, _ := multi.NewMulti("", nil, seq.DefaultConsensus)
	a, err := NewReader(r, m).Read()
	c.Check(err, check.Equals, nil)
	c.Check(a.Rows(), check.Equals, 11)
}

开发者ID:gordon，项目名称:biogo，代码行数:7，代码来源:alignio_test.go

示例5: main

func main() {
	flag.Parse()
	if *exclude == "" {
		flag.Usage()
		os.Exit(1)
	}

	nameSet := make(map[string]struct{})
	f, err := os.Open(*exclude)
	if err != nil {
		log.Fatalf("failed to open exclude file %q: %v", *exclude, err)
	}
	ls := bufio.NewScanner(f)
	for ls.Scan() {
		nameSet[ls.Text()] = struct{}{}
	}
	err = ls.Err()
	if err != nil {
		log.Fatalf("failed to read exclude file: %v", err)
	}

	sc := seqio.NewScanner(fasta.NewReader(os.Stdin, linear.NewSeq("", nil, alphabet.DNA)))
	for sc.Next() {
		s := sc.Seq().(*linear.Seq)
		if _, ok := nameSet[s.ID]; ok {
			continue
		}
		fmt.Printf("%60a\n", s)
	}
	if err := sc.Error(); err != nil {
		log.Fatalf("error during gff read: %v", err)
	}
}

开发者ID:kortschak，项目名称:loopy，代码行数:33，代码来源:keelhaul.go

示例6: ExampleSet_AppendEach

func ExampleSet_AppendEach() {
	ss := [][]alphabet.Letter{
		[]alphabet.Letter("ACGCTGACTTGGTGCACGT"),
		[]alphabet.Letter("ACGACTGGGACGT"),
		[]alphabet.Letter("ACGCTGACTGGCCGT"),
		[]alphabet.Letter("GCCTTTGCACGT"),
	}
	set = make(Set, 4)
	for i := range set {
		set[i] = linear.NewSeq(fmt.Sprintf("example DNA %d", i), ss[i], alphabet.DNA)
	}
	as := [][]alphabet.QLetter{
		alphabet.QLetter{L: 'A'}.Repeat(2),
		alphabet.QLetter{L: 'C'}.Repeat(2),
		alphabet.QLetter{L: 'G'}.Repeat(2),
		alphabet.QLetter{L: 'T'}.Repeat(2),
	}

	set.AppendEach(as)

	for _, s := range set {
		fmt.Printf("%-s\n", s)
	}
	// Output:
	// ACGCTGACTTGGTGCACGTAA
	// ACGACTGGGACGTCC
	// ACGCTGACTGGCCGTGG
	// GCCTTTGCACGTTT
}

开发者ID:gordon，项目名称:biogo，代码行数:29，代码来源:set_example_test.go

示例7: main

func main() {
	flag.Parse()
	if *in == "" {
		flag.Usage()
		os.Exit(1)
	}

	f, err := os.Open(*in)
	if err != nil {
		log.Fatalf("failed to open %q: %v", *in, err)
	}
	events := make(map[string][]*gff.Feature)
	fsc := featio.NewScanner(gff.NewReader(f))
	for fsc.Next() {
		f := fsc.Feat().(*gff.Feature)
		fields := strings.Fields(f.FeatAttributes.Get("Read"))
		if len(fields) != 3 {
			log.Fatalf("bad record: %+v", f)
		}
		events[fields[0]] = append(events[fields[0]], f)
	}
	if err := fsc.Error(); err != nil {
		log.Fatalf("error during gff read: %v", err)
	}
	f.Close()

	for _, ref := range flag.Args() {
		f, err = os.Open(ref)
		if err != nil {
			log.Fatalf("failed to open reference %q: %v", ref, err)
		}
		ssc := seqio.NewScanner(fasta.NewReader(f, linear.NewSeq("", nil, alphabet.DNA)))
		for ssc.Next() {
			seq := ssc.Seq().(*linear.Seq)
			for _, f := range events[seq.Name()] {
				fields := strings.Fields(f.FeatAttributes.Get("Read"))
				if len(fields) != 3 {
					log.Fatalf("bad record: %+v", f)
				}
				start, err := strconv.Atoi(fields[1])
				if err != nil {
					log.Fatalf("failed to get start coordinate: %v", err)
				}
				end, err := strconv.Atoi(fields[2])
				if err != nil {
					log.Fatalf("failed to get end coordinate: %v", err)
				}
				tmp := *seq
				tmp.ID += fmt.Sprintf("//%d_%d", start, end)
				tmp.Seq = tmp.Seq[start:end]
				fmt.Printf("%60a\n", &tmp)
			}
		}
		if err := ssc.Error(); err != nil {
			log.Fatalf("error during fasta read: %v", err)
		}
		f.Close()
	}
}

开发者ID:kortschak，项目名称:loopy，代码行数:59，代码来源:catch_global.go

示例8: SetUpSuite

func (s *S) SetUpSuite(c *check.C) {
	MaxKmerLen = 14
	s.Seq = linear.NewSeq("", nil, alphabet.DNA)
	s.Seq.Seq = make(alphabet.Letters, testLen)
	for i := range s.Seq.Seq {
		s.Seq.Seq[i] = [...]alphabet.Letter{'A', 'C', 'G', 'T', 'a', 'c', 'g', 't'}[rand.Int()%8]
	}
}

开发者ID:gordon，项目名称:biogo，代码行数:8，代码来源:kmerindex_test.go

示例9: ExampleNewMulti

func ExampleNewMulti() {
	m, err := NewMulti("example multi",
		[]seq.Sequence{
			linear.NewSeq("example DNA 1", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.DNA),
			linear.NewSeq("example DNA 2", []alphabet.Letter("ACGGTGACCTGGCGCGCAT"), alphabet.DNA),
			linear.NewSeq("example DNA 3", []alphabet.Letter("ACGATGACGTGGCGCTCAT"), alphabet.DNA),
		},
		seq.DefaultConsensus)

	if err != nil {
		return
	}

	fmt.Printf("%- s\n\n%-s\n", m, m.Consensus(false))
	// Output:
	// ACGCTGACTTGGTGCACGT
	// ACGGTGACCTGGCGCGCAT
	// ACGATGACGTGGCGCTCAT
	//
	// acgntgacntggcgcncat
}

开发者ID:gordon，项目名称:biogo，代码行数:21，代码来源:multi_example_test.go

示例10: getFasta

func getFasta(fn string) (seq.Sequence, error) {
	fasta_file, err := os.Open(fn)
	if err != nil {
		fmt.Println("Erro ao ler o arquivo", err)
	}
	defer fasta_file.Close()
	var s []alphabet.Letter
	t := linear.NewSeq("", s, alphabet.Protein)
	reader := fasta.NewReader(fasta_file, t)
	seq, _ := reader.Read()
	return seq, nil
}

开发者ID:jgcarvalho，项目名称:ASAnative_amber，代码行数:12，代码来源:ASAamb.go

示例11: writeFlankSeqs

// writeFlankSeqs writes fasta files containing the sequence of unmapped flanks
// identified in the primary hits provided. cutoff specifies the minimum sequence
// length to consider. left and right specify the filenames for the left and right
// flank fasta sequence files.
func writeFlankSeqs(reads string, hits hitSet, cutoff int, left, right string) error {
	f, err := os.Open(reads)
	if err != nil {
		return err
	}
	defer f.Close()

	lf, err := os.Create(left)
	if err != nil {
		return err
	}
	rf, err := os.Create(right)
	if err != nil {
		return err
	}

	r := fasta.NewReader(f, linear.NewSeq("", nil, alphabet.DNA))
	sc := seqio.NewScanner(r)
	for sc.Next() {
		seq := sc.Seq().(*linear.Seq)
		h, ok := hits[seq.Name()]
		if !ok {
			continue
		}

		all := seq.Seq
		if h.qStart >= cutoff {
			seq.Seq = all[:h.qStart]
			_, err := fmt.Fprintf(lf, "%60a\n", seq)
			if err != nil {
				return err
			}
		}
		if h.qLen-h.qEnd >= cutoff {
			seq.Seq = all[h.qEnd:]
			_, err := fmt.Fprintf(rf, "%60a\n", seq)
			if err != nil {
				return err
			}
		}
	}
	err = sc.Error()
	if err != nil {
		return err
	}
	err = lf.Close()
	if err != nil {
		return err
	}
	return rf.Close()
}

开发者ID:kortschak，项目名称:loopy，代码行数:55，代码来源:loopy.go

示例12: readFasta

func readFasta(fn string) (name string, seq string, err error) {
	fFasta, err := os.Open(fn)
	defer fFasta.Close()
	if err != nil {
		return "", "", err
	}
	t := linear.NewSeq("", nil, alphabet.Protein)
	reader := fasta.NewReader(fFasta, t)
	s, err := reader.Read()
	if err != nil {
		return "", "", err
	}
	sl := s.(*linear.Seq)
	return sl.Name(), sl.String(), nil
}

开发者ID:jgcarvalho，项目名称:gPHydro，代码行数:15，代码来源:gPHydro.go

示例13: readContigs

func readContigs(file string) (map[string]int, error) {
	f, err := os.Open(file)
	if err != nil {
		return nil, err
	}
	lengths := make(map[string]int)
	sc := seqio.NewScanner(fasta.NewReader(f, linear.NewSeq("", nil, alphabet.DNA)))
	for sc.Next() {
		s := sc.Seq()
		lengths[s.Name()] = s.Len()
	}
	if err != nil {
		log.Fatalf("error during fasta read: %v", err)
	}
	return lengths, nil
}

开发者ID:kortschak，项目名称:loopy，代码行数:16，代码来源:rinse.go

示例14: Clone

func (r Row) Clone() seq.Sequence {
	b := make([]alphabet.Letter, r.Len())
	for i, c := range r.Align.Seq {
		b[i] = c[r.Row]
	}
	switch {
	case r.Row < 0:
		panic("under")
	case r.Row >= r.Align.Rows():
		panic("bang over Rows()")
	case r.Row >= len(r.Align.SubAnnotations):

		panic(fmt.Sprintf("bang over len(SubAnns): %d %d", r.Row, len(r.Align.SubAnnotations)))
	}
	return linear.NewSeq(r.Name(), b, r.Alphabet())
}

开发者ID:gordon，项目名称:biogo，代码行数:16，代码来源:alignment.go

示例15: readContigs

func readContigs(file string) (map[string]*linear.Seq, error) {
	f, err := os.Open(file)
	if err != nil {
		return nil, err
	}
	seqs := make(map[string]*linear.Seq)
	sc := seqio.NewScanner(fasta.NewReader(f, linear.NewSeq("", nil, alphabet.DNAgapped)))
	for sc.Next() {
		s := sc.Seq().(*linear.Seq)
		seqs[s.ID] = s
	}
	if err != nil {
		return nil, err
	}
	return seqs, nil
}

开发者ID:kortschak，项目名称:loopy，代码行数:16，代码来源:reefer.go

示例16: main

func main() {
	flag.Parse()
	if *in == "" {
		flag.Usage()
		os.Exit(1)
	}

	f, err := os.Open(*in)
	if err != nil {
		log.Fatalf("failed to open %q: %v", *in, err)
	}
	defer f.Close()

	names := make(map[string][]string)

	sc := seqio.NewScanner(fasta.NewReader(f, linear.NewSeq("", nil, alphabet.DNAgapped)))
	for sc.Next() {
		seq := sc.Seq().(*linear.Seq)
		idx := strings.LastIndex(seq.ID, "/")
		names[seq.ID[:idx]] = append(names[seq.ID[:idx]], seq.ID[idx+1:])
	}
	if err := sc.Error(); err != nil {
		log.Fatalf("error during fasta read: %v", err)
	}
	f.Close()

	base := filepath.Base(*in)
	unique, err := os.Create(base + ".unique.text")
	if err != nil {
		log.Fatalf("failed to create %q: %v", base+".unique.text", err)
	}
	defer unique.Close()
	nonUnique, err := os.Create(base + ".non-unique.text")
	if err != nil {
		log.Fatalf("failed to create %q: %v", base+".non-unique.text", err)
	}
	defer nonUnique.Close()
	for name, coords := range names {
		switch len(coords) {
		case 0:
		case 1:
			fmt.Fprintln(unique, name)
		default:
			fmt.Fprintf(nonUnique, "%s\t%v\n", name, coords)
		}
	}
}

开发者ID:kortschak，项目名称:loopy，代码行数:47，代码来源:dedup_ccs.go

示例17: main

func main() {
	flag.Parse()
	if *in == "" {
		flag.Usage()
		os.Exit(1)
	}

	inFile, err := os.Open(*in)
	if err != nil {
		log.Fatalf("failed to open input:%v", err)
	}
	defer inFile.Close()
	*in = filepath.Base(*in)

	sc := seqio.NewScanner(fasta.NewReader(inFile, linear.NewSeq("", nil, alphabet.DNA)))

	var i, size int
	out, err := os.Create(fmt.Sprintf("%s-%d.fa", *in, i))
	for sc.Next() {
		if sc.Seq().Len() < *cut {
			continue
		}
		if size != 0 && size+sc.Seq().Len() > *bundle {
			err = out.Close()
			if err != nil {
				log.Fatalf("failed to close file bundle %d: %v", i, err)
			}
			i++
			size = 0
			out, err = os.Create(fmt.Sprintf("%s-%d.fa", *in, i))
			if err != nil {
				log.Fatalf("failed to open file bundle %d: %v", i, err)
			}
		}
		size += sc.Seq().Len()
		fmt.Fprintf(out, "%60a\n", sc.Seq())
	}
	if sc.Error() != nil {
		log.Fatal(sc.Error())
	}
	err = out.Close()
	if err != nil {
		log.Fatalf("failed to close file bundle %d: %v", i, err)
	}
}

开发者ID:kortschak，项目名称:loopy，代码行数:45，代码来源:bundle.go

示例18: metaSeq

func (r *Reader) metaSeq(moltype, id []byte) (seq.Sequence, error) {
	var line, body []byte

	var err error
	for {
		line, err = r.r.ReadBytes('\n')
		if err != nil {
			if err == io.EOF {
				return nil, err
			}
			return nil, &csv.ParseError{Line: r.line, Err: err}
		}
		r.line++
		line = bytes.TrimSpace(line)
		if len(line) == 0 {
			continue
		}
		if len(line) < 2 || !bytes.HasPrefix(line, []byte("##")) {
			return nil, &csv.ParseError{Line: r.line, Err: ErrBadSequence}
		}
		line = bytes.TrimSpace(line[2:])
		if unsafeString(line) == "end-"+unsafeString(moltype) {
			break
		} else {
			line = bytes.Join(bytes.Fields(line), nil)
			body = append(body, line...)
		}
	}

	var alpha alphabet.Alphabet
	switch feat.ParseMoltype(unsafeString(moltype)) {
	case feat.DNA:
		alpha = alphabet.DNA
	case feat.RNA:
		alpha = alphabet.RNA
	case feat.Protein:
		alpha = alphabet.Protein
	default:
		return nil, ErrBadMoltype
	}
	s := linear.NewSeq(string(id), alphabet.BytesToLetters(body), alpha)

	return s, err
}

开发者ID:gordon，项目名称:biogo，代码行数:44，代码来源:gff.go

示例19: TestWriteFasta

func (s *S) TestWriteFasta(c *check.C) {
	fa := fas[0]
	b := &bytes.Buffer{}
	w := NewWriter(b, 60)

	seq := linear.NewSeq("", nil, alphabet.Protein)

	var n int
	for i := range expectN {
		seq.ID = expectN[i]
		seq.Seq = expectS[i]
		_n, err := w.Write(seq)
		if err != nil {
			c.Fatalf("Failed to write to buffer: %s", err)
		}
		n += _n
	}

	c.Check(n, check.Equals, b.Len())
	c.Check(string(b.Bytes()), check.Equals, fa)
}

开发者ID:gordon，项目名称:biogo，代码行数:21，代码来源:fasta_test.go

示例20: mangle

func mangle() {
	seen := make(map[string]bool)
	hash := sha1.New()
	sc := seqio.NewScanner(fasta.NewReader(os.Stdin, linear.NewSeq("", nil, alphabet.DNA)))
	for sc.Next() {
		s := sc.Seq().(*linear.Seq)
		if s.Desc == "" {
			s.Desc = s.ID
		} else {
			s.Desc = fmt.Sprintf("%s %s", s.ID, s.Desc)
		}
		hash.Write([]byte(s.Desc))
		s.ID = fmt.Sprintf("%040x", hash.Sum(nil))
		if seen[s.ID] {
			log.Fatalf("duplicate sha1: %s", s.ID)
		}
		seen[s.ID] = true
		hash.Reset()
		fmt.Printf("%60a\n", s)
	}
}

开发者ID:kortschak，项目名称:loopy，代码行数:21，代码来源:mangle.go

注：本文中的github.com/biogo/biogo/seq/linear.NewSeq函数示例整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。